VMD-L Mailing List

From: Smith, Harper E. (smith.12510_at_buckeyemail.osu.edu)
Date: Sun Jun 26 2022 - 17:49:38 CDT

Hi Raman,

You can use the "DynamicBonds" representation in VMD and change the distance cutoff.

HTH,
Harper
________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Raman Preet Singh <ramanpreetsingh_at_hotmail.com>
Sent: Sunday, June 26, 2022 2:07 PM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Visualisation of CG bonds

Dear All, I have run a CG simulation in Gromacs using Martini FF and would like to visualise the trajectory in VMD. There's a Tcl script available on Martini website but that keeps on returning errors (with both, the .tpr file and the .top

Dear All,

I have run a CG simulation in Gromacs using Martini FF and would like to visualise the trajectory in VMD. There's a Tcl script available on Martini website but that keeps on returning errors (with both, the .tpr file and the .top file). The errors have been reported by others also but the fixed used by others have not worked in my case.

As I understand,VMD draws bonds based on a distance based cutoff. I was wondering if there is a way to draw long bonds, as is typical in CG MD, in VMD. In case VMD can not do that, is there any other visualiser that can be of help.

Regards,
Raman